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The Biosystems Informatics Institute (Bii), and its commercial trading arm Turbinia Limited, has signed a collaborative alliance with Lucidyx LLC. Bii will assist Lucidyx in the further development of two key integration products that enable life science software developers who develop tools that access genomic data through either Oracle(R) or through application programming interfaces (APIs) to conveniently and transparently query and retrieve information from Searcher(TM), a next-generation genomic annotation search engine developed by Lucidyx.

Initially, the collaboration will focus on the development of Lucidyx Oracle(R) Gateway(TM), a bridge between Oracle(R) and the Lucidyx search engine, allowing Oracle(R) SQL queries to combine data from Oracle(R) with data from Searcher(TM) as if all the data was stored in Oracle(R) tables. This integration is done at the SQL level so it is easy for the user to write sophisticated queries linking their data in Oracle to genomic annotations accessed via Searcher.

The second product, Lucidyx Puma(TM) will facilitate access to the Lucidyx search engine for programmers using Java or Perl, through http, or through a command-line program. The API follows the well known SRS(TM) getz/wgetz syntax, thus both lessening the learning curve and simplifying the conversion of legacy code.

Bii and Lucidyx are already in discussions with several top-tier pharmaceutical companies for potential licensing of the products.

"In recognition of the needs of life science software developers to access genomic data through either SQL queries or through application programming interfaces (APIs), we are developing two additional software products," said Manuel J. Glynias, president and CEO of Lucidyx. "The Lucidyx Oracle(R) Gateway and Lucidyx Puma(TM), will facilitate access to the Lucidyx search engine by life science programmers through either Oracle/SQL or through a well known API. In each case, the syntax has been designed to feel familiar to users, while delivering lightning fast, more complete, searches, and while running on a wide variety of low-cost platforms."

"These tools are critical as we attempt to better contextualize off-target drug effects and further understand the data flowing from proteomics and transcriptomics experiments across the industry," noted Ian Humphrey-Smith, Chief Executive Officer of the Bii. "Our 'slot-out / slot-in' solution will minimize barriers to customer uptake by providing accessibility via legacy and contemporary methods, including SRS(TM) wgetz and Oracle(R) SQL. Such interfaces will be essential to allow integration of diverse databases within pharma with applications such as Lucidyx Searcher(TM).

Lucidyx Searcher(TM) has minimal performance overhead and high-speed prototypes are already available for evaluation. These features will make it easy for customers to combine our more rapid, feature-rich searches of life-science information with their existing databases and applications."

Searcher(TM) is a web-based application with a powerful search engine that allows users to more rapidly find, view, analyze and save relevant entries in any genomic database. It also includes auto-updating capabilities, as well as automated versioning and archiving, thereby minimising data loss. Customers using the two compatibility products will be able to take advantage of the more rapid and feature-rich search-and-retrieve functionality that Searcher(TM) provides without having to change their existing infrastructure, thereby providing an invaluable bioinformatics audit trail that will become increasingly critical as pharma clients consider the ramifications of Voluntary Genomic Data Submissions to the FDA.

About Lucidyx

Lucidyx LLC is a Cleveland, Ohio-based corporation whose mission is to develop software that allows researchers to leverage genomic information in their daily work. Its lead product development, Searcher(TM) combines annotation, homology, publication, web and sequence motif searching, and provides the means to combine and store these searches while also enabling the manipulation of both individual objects and sets of objects.

For more information, visit or call 440/212-1125.

About the Bii

The Biosystems Informatics Institute (Bii) is a new UK research establishment that, along with its commercial trading arm, Turbinia Limited, is focused on the delivery of systems biology and bioinformatics software tools to enable the development of better drugs and healthcare delivery. The Bii boasts links with several regional partners including One NorthEast; the Universities of Durham, Newcastle, Northumbria, Sunderland and Teesside; and Nonlinear Dynamics, a world leader in the provision of proteomics software.

For additional information, visit This initiative is funded by the UK Department of Trade and Industry and One NorthEast.

For more information, visit
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Publication:Online Product News
Date:Sep 1, 2005

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